You can actually fill these bubbles if they are of appreciable size. Small bubbles, below 1/4" should be left alone; they don't factor into getting a good figure at all.

For those BIG ones, you can slightly heat up some pitch until it is like warm taffy and won't hurt your hands and stuff a wad into your lap so it is slightly higher than the general curve of the lap.

Gently hot press, (I like to think of it as "warm" pressing), and the bubbles will fill in to the level of your lap. There may be a round seam, but after an hour of polishing, you might have a very hard time trying to see it.

Now that I am thinking of it, you might have the opposite problem of bubbles rising above the surface of the pitch. In all cases these are air bubbles. Gently "pop" them with a razor blade and then press to see if any pockets need filling in, as mentioned above.

If these bubbles are solid, you've got something in your pitch that doesn't belong there, but this is very unlikely to happen.

I was going to say the same thing as Ed did .How big are the holes? A picture would help.Not a big problem, fill them up with a tiny bit of pitch and do a worm press untill the surface is even and you're ready to polish. Anyway you'll discover as you polish that the lap will get thinner after so much pressing and channel recutting so the small holes will disappear.

If the bubble is into the pitch forming a trapped air pocket, I would just connect the pocketed area to the nearest pitch groove by cutting a channel to the groove with a razor blade. If you haven't cut your grooves yet, see if you can locate one of your grooves right through the bubbled area. I have found that small pockets will eventually pressed out by the end of polishing.